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Tuesday, March 7, 2017

Neolithic Europe: it's complicated (Lipson et al. 2017 preprint)

The dam is breaking. Just in at bioRxiv:

Abstract: Ancient DNA studies have established that European Neolithic populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date---a total of 177 samples, 127 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000-2900 BCE, n = 98), Germany (5500-3000 BCE, n = 42), and Spain (5500-2200 BCE, n = 37)---we investigate the population dynamics of Neolithization across Europe. We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions.

Lipson et al., Parallel ancient genomic transects reveal complex population history of early European farmers, bioRxiv, Posted March 6, 2017, doi: https://doi.org/10.1101/114488
Update 08/03/2017: In fact, there's nothing overly complicated in this manuscript. The table below says it all: Neolithic farmers across space and time in most of Europe were very closely related, and only differed in their levels of Western Hunter-Gatherer (HG) admixture. Admittedly, things would look a lot simpler if not for that somewhat unexpected R, R1 and R1b1 in Middle Neolithic Germany, but this doesn't appear to be a game changer, and is not flagged as such in the preprint.

85 comments:

Balterhohle is interesting. The data indicates the people buried there were the fusion of a hunter gatherer tribe and farmer tribe. Some lived as hunter gatherers, some as farmer-hunters, but all were heavily admixed between both tribes.

But the R1b1a2-M269 from Iberia is confirmed against all what Rocca said against ne and Genetiker. It seems to me that everything is becoming clear now. And let's wait that also Italy is tested at the level of the other countries...

I thank you, I have to read the paper yet. That R-V88 was in Iberia, and that it came from Italy, is just my theory that I think having demonstrated, but we were discussing also about another possible R-M269 from Iberia. But the presence of WHG and specifically of Villabruna in these samples seems that is going in favour of my theory. We'll see...

Interesting that we see more R1b ; does add putential nuance to later M269 expansion. We have Baltic Mesolithic R1b, west German Mesolithic admixed MNE R1b, north Italian LUP R1b... None in the Balkans (all I lenages); and 0 from 2 in Ukraine Mesolithic (which were R1a and I2).

I recall Frank N predicting this about the fisher -Foragers from north Central Europe ...

We'll see what it will be found in the Italo-Celtic languages places (I think from Italy to Iberia northward). I am asking from so long that Rinaldone, Arene Candide are tested. Of course if no R1b will be found, we should think to a late migration from East or elsewhere: ahahahahahah.

Of course, Bletterhole is the closest to HG, but La Brana wasn't R1b. We may think that I was right in saying that R1b survived in the Italian Refugium, but we have to find it yet in the ancestors of Bletterhole if they came Southward...

Difficult to agree with you, even though that they broght Westward the Language but not the R1b could be well accepted to me, but I think that Yamnaya was the satem IE languages, brought up there from the R-L23 from the Italian Refugium. You'll see that I put all in the sack also about linguistis,,,

Well, R1b looks proto-WHG at least. Look at the supplementary data figue. EHG is now 61% proto-WHG & 39% MA-1.Collectively, R1b looks WHG, even if some drifted onto the steppe at some point, and perhaps expanded back west.

How would you know this? There's nothing out there suggesting R1b wasn't present in early Indo Europeans. If one agrees with the Kurgan hypothesis, then R1b has been found in the earliest Indo Europeans.

"R1b looks WHG, even if some drifted onto the steppe at some point"

Even though Mesolithic, Copper age, and Bronze age Samara was full of R1b? Narva had EHG admixture, that could explain its R1b.

Also we don't know the relationship between EHG and WHG. They weren't two completely distinct races. They were closely related, their ancestry intersected a lot in the Paleolithic. How do you know WHG isn't part ANE or part something from hence EHG got its R1b?

What this study did is get the genomes of mtDNA samples from old studies and get genomes from new samples whose DNA hasn't been sequenced but from the same locations and periods as samples whose DNA has been sequenced.

They really should have gotten Neolithic genomes from unstudied regions like Eastern Europe and Italy.

"R1b is NOT IE...""You R1b people don't want to be the conquered but you ARE ..."

1) Bear in mind a lot of people prefer the idea of paleolithic continuity.

2) Personally i've always thought the Atlantic west was last conquered by La Tene in the iron age however many earlier stages there had been before that - however those earlier stages are still interesting if you're a history nerd.

3) I think some R1b is PIE and some not*.

*I think most people survived the ice age in refuges near water (cos fish are cold blooded) but i also think some survived in the interior cos megafauna. When the megafauna were done for (earlier west of the Urals than east) the western half of those people had to move into the near water refuges. Hence some clades of R1b around the European coast e.g. Villabruna, and some clades around the northen shores of the Black and Caspian seas. I think the clades around the Black and Caspian seas became part of PIE (cos horses).

4) Last but not least

"Admittedly, things would look a lot simpler if not for that somewhat unexpected R1 and R1b in Middle Neolithic Germany..."

I expected (probably minor or extinct) clades of R1b to show up more or less randomly in Europe either from the refugee mammoth hunter reason or the neolithic jewelry trader reason.

@ Richard RoccaGioiello said... "But the R1b1a2-M269 from Iberia is confirmed against all what Rocca said against me and Genetiker.

Given that they used the ISOGG tree last month, R1b1a2 is indeed V88 and not M269. That must be very embarrassing for you".

Samuel Andrews already made me note that, and I replied him. I hadn't read the paper yet, but I read it very carefully now. If there is something embarassing very likely is for you, seen that all my theories seem confirmed and yours denied. You were so prostate that you announced leaving the "Italy FTDNA Project". But it isn't necessary: so that you are or you aren't the sum is the same: 0.

No regrets helping hundreds of people who sought my help on the Italy project (including you). A classy guy you are, right to the end.

So you argued for a M269 equivalent all this time and now that it isn't you brush it off like its nothing, just like you did with the I2 Remedello samples and Otzi??? Funny. By the way, where are all those Iberian L51s that you said were derived from Italian Cardial Culture? Surely you are not going to say that there aren't enough samples again, are you? Again, very embarrassing what has become of your theories.

What does separate a scientist as I am from a "lackey" as you are? That a scientist read all what has been published on an argument, and the lackey does other. If you had read my posts, not all the 10 or 20000 I wrote, but only the few ones of this thread, you would have known what I said: that this samples are all from Northern Iberia, i.e. not from the places colonized from agriculturalists from Italy of 7500 years ago (except the R-V88 and perhaps some G and I etc.) and all the Bell Beakers places lack, Central and Southern Iberia, Southern France and the Whole Italy. We are waiting that all the PhDs linked to your "firm" one day test them too.

Till Rocca (FTDNA) and Rohlfsen (Harvard PhDs) entered the argument, I discussed only of genetics, and, even though Rocca doesn't mind if someone call Italy a "sink", I mind, and hope one day to meet this figure somewhere. I am 69, but I hope that that happens.

That's still probably not the most likely scenario! By a very long shot. Still seems more likely that European R1b came from a steppe clan outside Europe (including Eastern Europe) which we haven't sampled.

But the possibility is there that European R1b came ultimately from a European HG / Europe MN individual whose descendents then experienced powerful growth through the Bronze Ages (potentially to the point of sidelining the "real" early R1b from the steppe). Though this would have had to have already happened by the era of the Bell Beakers, if so...?

@ Nirjar007: The star-like expansions in R1b we see are likely to have happened in an Indo-European speaking population. (It is likely to be the signature of a "conqueror" individual and his extended clan, just as South Asian R1a is).

Did the ultimate ancestor of that R1b individual speak a language ancestral to Indo-European? Very likely not. Villabruna almost certainly didn't, and his common ancestor with other, later forms of R1b didn't.

Though, if it does turn out to be true that European R1b was from WHG or MN, not a steppe population, that would probably make Europeans even less descended from foreign "conquerors" and people subjugated by foreign "conquerors" on balance (if that's even a sensible model), than we think at the moment, as it would indicate that at least in some areas, their MN and WHG ancestors turned the tables a bit.

Sam Andrews: They really should have gotten Neolithic genomes from unstudied regions like Eastern Europe and Italy.

Hungary, Latvia and Lithuania are in Eastern Europe, as is Russia, and are pretty heavily studied (more so than, e.g. France). So you can only be talking about Ukraine ;). I much more agree the lack of anything substantial below the 43rd parallel (in Spain, or Italy, or the Balkans) really sucks still, as these are the routes by which Early Neolithic populations must have entered Europe... Technically it must be very challenging, more so than their Near Eastern effort. The Balkans paper later this year will help to begin redress this.

"We computed pairwise outgroup f3-statistics, performed multidimensional scaling (MDS) on the resulting matrix, and converted the MDS positions to polar coordinates (Supplementary Information section 5). The correlation between genetic structure and longitude revealed by this analysis (Figure 1D) suggests that our reference samples can reasonably be used to define a geographic cline among hunter-gatherers within Europe."

I've been thinking for a while that this would be really interesting to do (and really easy) with a matrix of f3 statistics and the Principal Coordinates Analysis (User Defined Similarity) function in PAST3, to see what it would produce, and that's how they get their figure S6.1 - http://i.imgur.com/TwSPUbG.png (which they converted into polar coordinates to get their Figure 5).

If you wanted to take this further, adding the SHG and the new Lithuanian, Latvian and Ukrainian HG and EHG (or even AG3) samples might produce a cool result, and one which might confirm or contradict their result, and wouldn't involve running many f3 statistics.

"Both populations" (Iberia_MN and Iberia_CA) "have evidence of ancestry related to LB1 and to a different WHG individual, suggesting that in contrast to the earlier admixture," Iberia_EN "the large increase in hunter-gatherer ancestry between the EN and MN had a non-local origin.

I wonder if this relates to the Atlantic Megalithic phenomenon, and the early 4000-3000 BC split into a "Europe of Jade" and "Europe of Copper and Gold" (https://www.researchgate.net/figure/273490638_fig1_Fig-1-Comparative-distribution-across-Europe-of-the-large-jade-alpine-axes-green).

That is, French WHG ancestry comes to Iberia with the inclusion of Iberia into a wider trade / political system reaching outside of Iberia. (French HG ancestry perhaps more akin to Loschbour, Rochedane, Ranchot from NE France-Belgium which form a relatively tight f3 sharing cluster?)

Or even potentially links to early Chalcolithic SE Europe?

Maju, you may find something to think about here, if you're reading...

@David - your treemix runs had Villabruna come back as 5% steppe admixed, right? Any chance you can confirm the results in this paper that have KO-1 as ~9% EHG (or rather about 4% ANE)? It'd be interesting to know to what extend steppe ancestry was bleeding into eastern WHG (KO-1 and Villabruna) and EEF populations in the early Neolithic. It would be very interesting to check those Bla samples (particularly Bla8) for steppe ancestry too.

@Matt: "That is, French WHG ancestry comes to Iberia with the inclusion of Iberia into a wider trade / political system reaching outside of Iberia. (French HG ancestry perhaps more akin to Loschbour, Rochedane, Ranchot from NE France-Belgium which form a relatively tight f3 sharing cluster?) "

See extended figure 2 - it looks like the new WHG admixture drags the Iberian Chaloclithic samples towards KO-1 and Villabruna. Lochsbour doesn't seem to be far enough east.

@ Ryan, are we talking about page 29 of the PDF or 32 (Extended Data Figure 2 just HG ancestry plotted against latitude and longitude of samples)?

If we're talking the page 29 tables, it looks like their model is EN (10%): La Brana, MN (23%): La Brana+Loschbour, CA (27%) La Brana+Loschbour/KO1/Villabruna in main scaffold or just Villabruna in the alternative scaffold (suggests KO1 is probably a bit too far "east").

I'd probably assume from that it works as mostly La Brana in Early Neolithic, adding Loschbour in the Middle Neolithic (fitting with integration with Middle Neolithic France and the Atlantic). Assuming MN is mostly ancestral to CA, once the main trunk of admixture is done by the Middle Neolithic later in the Chalcolithic, perhaps some merging with populations from further afield in Italy and East-Central Europe (e.g. Remedello?)?

Although Ryan, for idea of Iberia_CA being more integrated with the Atlantic facade, North Germany / Sweden hgs might ultimately add a little more than KO1 / Villabruna... Ballynahatty and Sweden_MN farmers would good extensions to this work, if there's enough of them to work with.

In the supplementary information pdf they have a figure (S7.1) in which they model EHG as 61% pre-WHG and 39% ANE. Why R1b has to be from the ANE side? When we also have R1b in mesolithic western Europe (Villabruna), and also 2 Latvian Mesolithic samples were R1b (or maybe one of those was early neolithic, can't remember). In eastern Europe there was an EHG/WHG continuum, when R1a folks started moving west from the steppe the first people that they encounter probably were similar to the one sampled in the baltic paper. A varing WHG/EHG mix with maybe loads of R1b, also the right R1b. Ultimately R1b came from eastern Europe, no doubt about that, although the question about which people carried it first it is still up to debate, there is no definitive proof of anything at this point.

"I much more agree the lack of anything substantial below the 43rd parallel (in Spain, or Italy, or the Balkans) really sucks still, as these are the routes by which Early Neolithic populations must have entered Europe."

To find the origin of domestication you may want to look in the climate-zone where domestication was crucial to survival. Which takes you north of the 45th parallel - and back into the Paleolithic time-zone.

Considering the number of remains found from ancient domestication - such as grinders, cultivated plants and animals - it just so happens that a clear majority is found north of the 43rd parallel.

If the geneticians are right about the split of the first dogs from the grey wolf - as of 35.000+ years ago - there's no reason to doubt the domestication of goats and pigs to have a paleolithic origin, too.

Today we even know that Oat were in use during the LGM, since a 19.000 years old pollen was brushed out from a vey well documented site in Italy.

The NW European "Solutreans" that survived the LGM, to form the Magdalien-Hamburg-Pertuna communities were obviously able to benefit from this tradidition - in order to survive the cataclysmic climate-changes of Alleroed/Dryas/Holocene period - when the MEDIAN temperature over Greenland fell by more than 15* Celsius, the median of NW Europe fell only (!) by 9-10* C and the median of NE Asia fell by 11-12* C.

Mapping the present climate north of the 40th paralell we have a very clear NW-SE cline, due to the impact of the everlasting Gulf-stream, pushing surface-water of no less than +4 into the shores of the English Channel, the North Sea and the Scandinavian west-coast.

Today we find the northern limts of wheat-production at the west-coast of Norway - streching up to the 65th parallel. Moving east, into the Baltic, there's no wheat ripening above the 60th parallel. East of the Baltic Ocean you need to go even further south, gradually by steadily - until Bactrica and the Himalayan massive.

North of this border you need Barley and Rye - togteher with Goats and Sheep: while Oat - together with Cows and Horses - normally follow the Wheat.

As the oldest known burial-mounds - just as the oldest buried dogs, horses and oxes - are found at the western egde of this climate-zone, close to the famous Gulf-stream, we may induce that the survivors of the Younger Dryas were the first to introduce seasonal planning and agricultural organisations to the northern parts of Eurasia.

Which leaves us with the ONLY refugia on record, known to have survived the Younger Dryas north of the 40th parallel - at the shores between the English Channel and the Western Baltics.

Today we know that the first spread of settlements - as the Holocene climate established itself - can be traced to this refugia in the Western Baltics - from where it spread north to the North Cape as well as east to the Finnish Bay and along the Volga-river-route east to the Kas-berg/Caspian Sea.

Presumeably, the boat-cultures populating the rivers and coasts Europe (including the archipelagos of the North Atlantic and the Mediterreanean Sea) were descendants of the same refugia.

Following the dynastical structure of the y-dna-lines comming out of Ice-time, we may conclude that a specific selection of patrilinear lines were the organizing element in all these societies - from where ALL the 'advanced cultures' and consequent civilizations were formed. Thus we may reflect the various 'civilizations' to their respective 'kingdoms' and 'tribes' or 'aets' (aka aet-nicities) - as "general adaptions to gross environmental changes".

The mariners first populating the high-arctic areas of Eurasia were obviously of y-dna CF->I.

One of their brother-lines, y-dna G, were obviously respeonsible for re-populating the semi-arctic, South-West Eurasia - such as the Meds and the Black Sea. A third dynasty, based on y-dna J, seem to have pioneered the re-settlements of SE Eurasia, while their 'cousins' carrying y-dna H made it to the semi-tropic and tropic India, mixing with a tropical refugia of the Younger Dryas. When the arctic (Caucasian) travellers found the rivers of Aral they gradually reached the asian refugianst east of the Himalayas - as y-dna CF->K/O could mix with a proto-chineese population (mt-dna C/D) - and gradually bring the combine (mt C/Z) back to the shores of the Baltic, no later than 7.500 BP.

At this time the Holocene maximum had been effective for a gross millenia - providing lush grasslands for large flocks of cattles and horses - from Spain to Scandianvia and then again; onwards to the east, along the temperate climate-zone.

To digest milk and enjoy all kinds of diaries you need to breed people that are 'infantilized' - in order NOT to stop digesting the proteins, fats and sugars of milk - at the age of three. Digesting goats milk is one thing, digesting cows milk even harder. Which made it convenient to select males and females with these abilities to form their own, specific cultures and economies - based on one or more NEW dynasties; with specific talents regarding milk-consumption.

While y-dna G, H, I, J and K/MNO already built on goats and sheeps populating the woodlands, the K2/R started of with cows and horses, wheat and oat- en masse - on the wide Eurasian fields that started to turn massively green - from the west towards the east - as of 9.000 BP.

Please understand that they ALL kept on fishing and hunting - too, as salt and seafood is obligatory to ANY family, community or dynasty that want to reproduce itself. None-the-less; as time passed and large societies of agricultural 'specialists' grew up we got larger fishing-communities too, along the lakes, rivers and shores of the continent. Moreover - as the inland populations grew a common need of transport and trade grew simultaniously - to accomodate the nutritional need of the inlanders and highlanders.

Thus we find the oldest mariners up front as 'traders and transporters'. Which is why y-dna I keeps popping up in graveyards of dynasties of y-dna G, R and N. The close and enigmatic connection between all these 'caucasians' seems to agree that they do have a LCA from the end of ice-time. Which, as far as facts can tell, means the Younger Dryas - to which the LGM was nothing but a modest prelude. Eventhough the former brougth seals and pinguins down to the 43rd paralell and west to the Adriatic Sea, they both brougth reindeers and snowcats to both Spain and Italy...

@Matt - yes, page 29. In the early and middle neolithic only Lochsbour and/or La Brana were consistent with the WHG in Iberia in either model. In the chalcolithic that expands to include KO-1 and Villabruna. That's what they're talking about.

I'm not sure why migrations from sparsely inhabited places like Northern Germany or Sweden should be assumed though? Especially when cultures with the right genetic makeup were living in to the south.

@ Ryan, hard to assume anything either way. There are a range of potential cultures with probably appropriate longitude to Villabruna. It could be those within the Atlantic sphere where megalithism happened or you could have geneflow outside it, and the "Europe of Jade" sphere in the above graphic I linked goes right up to Central Germany anyways. (Blatterhohle get LO+K/V as its admixing fraction even though quite close geographically to Loschbour).

(Generally, I don't know where population density was the strongest or wasn't in that period. I wouldn't have expected Skara Brae in Orkney to be the origin of an expanding cultural complex, but apparently the theory today is it was.)

At the moment, it seems in ancient dna the solid deep link of R to ANE is MA-1 having R (basal to R1 / R2 or sidebranch), and then, in extremely simplified terms, so far you have WHG related cultures (EHG and WHG proper) usually in Eastern Europe, having the R1 descending clades, possibly from this ANE source, and Iran_Neolithic, which is highly diverged from WHG but seems to have some link to ANE, having R2.

My point was that exactly, that R1b could have risen in a mixed population, I think it is very very likely that the first man with R1b wasn't all ANE or all WHG. In eastern europe, in the baltics, in Scandinavia there was an ANE/WHG continuum, EHG are part of that, SHG is part of that, baltic hgs are part of that, Villabruna was a part of that. If you use the label "ANE" you are bound to make a factual mistake, beacuse the population that you are talking about was probably more WHG than ANE. R1b isn't that old after all, and we have no indication that pure ANE lived in Europe so recently. And r1b wasn't much older than Villabruna after all. It is possible, and I don't see the reason why it can't be the case, that R1b evolved in a mostly WHG population. Even EHG was mostly WHG, I think that ultimately the problem is a lack of awareness of the ANE/WHG continuum in Europe.

Please note that the climatical fluctations at the end of ice-time (23.000 - 12.000 yrs BP) strongly decimated all the largers species that existed during the Eurasian paleolithic.

At the very end of this extreme fluctations - during the Younger Dryas - the continent went through a "Megafaunal Mass-extinction Event" - where 2/3 of the mamalian species of Europe and northern Eurasia (above the 40th parallel) - such as giant deer, elk and mamoths - went completely EXTINCT.

A similar extinction is also recorded in the North Americas, during the very same millenia; 12.900 - 12.000 yrs BP.

Among the few surviviors were a bunch of humans, who apparently had a biology and a culture very well adapted to the cold and dim environment of ice-age Europe. Besides, among the large animals surviving where species like dogs and ducks, goats and cows, pigs and horses, deers and reindeers, wolves and wolverines, bears and beavers.

Half of them may have needed human assistance to manage the extremes of the YD. Which may explain the extensive use of domesticated animals that evolves as the arctic and semi-arctic climate-zones are re-populated.

Due to the extreme decimation of these species they all went through a generic and gentic bottle-neck during the Younger Dryas. Consequently we have a strong genetic "re-shuffle" (or "re-start") after the YD.

Checking the genetic maps of Eurasia before and after the LGM (23-18.000 yrs BP) we see a genetic re-shuffle. Then a similar and even stronger re-shuffle takes place with the YD.

Which means that the specific y-dna and mt-dna of the Paleolithic gene-pools were decimated and bottle-necked at least twice. Which again means that MOST of the dna-types and lines from Paleolithic samples are basically extinct - and thus "blindgates" in runs with mesolithic Eurasians and all their present descendants.

Which again begs the question of locating the Caucasian "urheimat", to explain the mesolithic, neolithic and present distribution of y-dna-lines.

Then we may find the origin of agriculture and the historical stem of the I-E languages to evolve from the same area of origin - as a quintessence of the traditions that made the genetic ancestors of the Caucasians able to survive 40.000 years of ice-time, north of the 55th parallel.

"At the moment, it seems in ancient dna the solid deep link of R to ANE is MA-1 having R (basal to R1 / R2 or sidebranch), and then, in extremely simplified terms, so far you have WHG related cultures (EHG and WHG proper) usually in Eastern Europe, having the R1 descending clades, possibly from this ANE source, and Iran_Neolithic, which is highly diverged"

I think that might place to much trust on a drifted, isolated, and extinct side-population. We have R1b in European ancients which lack ANE completely. Whilst even Gio agrees with an ultimate central Asian origin of R1, the link to Siberia and "ANE" seems to be a little shaky.

You all know that I was banned from Anthrogenica on 2013 and I cannot reply there, but I am seeing that also ADW_1981 thinks to be a geneticist

ADW_1981 replied to a thread Parallel ancient genomic transects reveal complex population history of early Europea in Ancient (aDNA) I can on Central Asia. https://yhrd.org/tools/branch/R1b-M335

I have written about R-M335 from at least 7 years, not only on blogs out now or which deleted my posts, but on the still living www.worldfamilies.net and www.eng.molgen.orgOf course R-M335, being at the level of R-L278, is diffused in all the Euroasiatic world and the first sample was found from Cinnioglu in Anatolia on 2004, but not only the first sample submitted to YFull is Italian Martinucci (just from Italian Alpine zone) but Central Europe, Scandinavia and Italy of course are plenty of this old haplogroup.

R1b was in Bolshemys culture.Which means that Kel'teminar could be full of R1b. And we have another early divergent branch in S Caucasus.R1b was simply too widespread to be linked to one component.But M269 expanded from one place.

Totally missed this. It looks like we might actually have some Iberian Bell Beaker samples in this paper. From the supp info, page 36...

Dolmen “El Sotillo” (Álava)

El Sotillo megalithic site is located in the Alava Rioja county (Basque country), between the limit of Laguardia-Guardia and Leza municipalities, at the south of the historical territory of Alava. The site is 617 meters above the sea level. It was discovered in 1955 by Domingo Fernández Medrano and excavated by himself, José Miguel Barandiran and Juan M. Apellániz in 1963 [90].

It is a megalithic tomb with a corridor and an almost circular chamber, formed by nine slab stones, a corridor and a tumulus of eleven meters of diameter. During the excavation, numerous lithic tools were uncovered, including six pedunculated arrowheads of silex, a bone and a metal arrowheads, a metal burin, retouched flakes, two fragments of foliaceous projectile points, etc. There are some Bell Beaker pottery remains and a cup with incised decorations.

The remains of thirteen individuals, including eleven adults (six of them males) were retrieved. The radiocarbon dates placed the initial use of the site at the Late Chalcolithic period, the Bell Beaker period (4390+30, 4350+30, 4040+30, 4000+40 BP). After a hiatus of about half a millennium, the usage of the structure as funerary place increased during the Middle Bronze Age period (3550+30, 3430+30, 3380+30, 3360+30, 3360+30, 3320+30, 3160+30, 3120+30 BP), with one date from the Late Bronze Age (2740+30 BP).

But where these samples tested would be? Perhaps they are saving them for the BB paper, and, anyway, pots doesn't mean men and women: they could belong to the same people tested here and not to BB people. But we'll see...

"The remains of thirteen individuals, including eleven adults (six of them males) were retrieved. The radiocarbon dates placed the initial use of the site at the Late Chalcolithic period, the Bell Beaker period (4390+30, 4350+30, 4040+30, 4000+40 BP). After a hiatus of about half a millennium, the usage of the structure as funerary place increased during the Middle Bronze Age period (3550+30, 3430+30, 3380+30, 3360+30, 3360+30, 3320+30, 3160+30, 3120+30 BP), with one date from the Late Bronze Age (2740+30 BP)".

Yes, 2 of the sites in Spain showed some Bell Beaker pottery, but they are mainly megalithic collective tombs, where some Bell Beakers were deposited at a late stage. I doubt we'll find any R1b in those kind of sites.

The ones from "La Chabola de la Hechicera" (Witch's hut) are too old (c. 3000 BC), but those ones from El Sotillo at least 2 of them are from 2400-2300, which could be the earliest to possibly find R1b. But they turned out I2a, and they're very low coverage.

There are dates from around 2400-2200 BC in Iberia that could have R1b Bell Beaker guys. But from a few specific sites, where you'll need single burials (or double, but not collective ones), with metal objects (knives, daggers, Palmela points. And gold). In English I could just find this paper about one possible site with early dates:

Concluding, the most evident difference between pre-Bell Beaker and Bell Beaker grave goods comes from: a) The generalization of the military panoply, with copper daggers, axes, and arrowheads (palmela). If we generalize on the basis of the data from La Vital where only the female burial lacked weapons, we may suggest a relationship between military panoply and an emphasis on the role that male individuals played in the society

Or sites like La Sima III, in Soria, where a mound with a double burial was found by a previous Neolithic collective burial*, with these kind of items:

The dating for these burials is 2458-2274 cal BC. One of the vessels was quite specific:

A unique Bell Beaker in Iberia, which was discovered in a single grave in the La Sima Mound (Miño de Medinaceli, Soria, Spain), is presented. The analysis of the decorative technique of this vessel suggests a reconsideration of the supposedly incised technique of the Ciempozuelos style Iberian Beakers. The lineal decorative pattern and the peculiar form of this vessel have their best parallels in the Brittany, and ultimately in the Corded Ware complex, in the context of long distance exchange systems through which Bell Beakers and accompanying objects (mainly gold jewellery) moved between the Brittany and Central Portugal, crossing the interior of Iberia.**

A few other sites with similar dates around 2400-2200 BC could be from R1b too, like some of the burials at the Valle de las Higueras, Toledo. But otherwise I think it will mostly be after 2200 or even 2000 BC.

@ Ron"Or EinSofOne of the Lengyels was E-M78, and has a call equivalent to EV13. Recall also that a couple of Spanish EN indivuals in Lacan were possibly EV13, based on STRs"

I am saying from so long that, even thought many thought that E-V13 came from the Balkans, Italy has the oldest haplotypes, also of E-L618, and E-V13 hasn't been found so far in the Balkans. We'll see if also about that I'll resulted right.Of course it may have come from everywhere...

@Jomon - I take your point, but keep in mind that given Villabruna is ANE-admixed, so it's likely that virtually every European from the mesolithic onward has some ANE admixture.

Y-haplogroups and aDNA can become a bit decoupled over time too. R and Q are pretty clearly linked to ANE (with the possible exception of R2). Their parent is haplogroup P, and P(xQ,xR) is found primarily in South East Asia, particularly in Indonesia and among the Negrito Aeta people in the Philippines.

The ancestor of P is K2b, and other than P itself, K2b is exclusively found in island SE Asia, particularly in Papua New Guinea, Australia, Indonesia and again among the Aeta.

K2b's ancestor is K2, and other than K2 itself, its descendants are found exclusively in East Asian and East Asian-admixed Siberian populations.

So if R/Q are ANE, its ancestors are Papuan and something close to that. I'm personally R1b-M222, a descendant of some sort of Papuan-like man living perhaps 30-40,000 years ago who had some close relationship with the ancestors of East Asians. Up to Villabruna 14,000 years ago, you can still detect that increased affinity to East Asians, but today that thread is mostly lost on the aDNA side. So it's quite possible to find populations with haplogroups that don't really match what we might expect from their aDNA.

There's also the Chadic populations in Africa that are dominated by R1b with little or no detectable ANE. They certainly have some ANE ancestors, but over time most of that DNA has been washed out.

"The R sublclades of chadians are very young (~ 5Ky) and received from levantians migrants with already very diluted or lacking ANE"

Again! R-V88 is documented in Italy during the Palaeolitic and expanded after the Younger Dryas. Italian samples are the oldest ones: R-V88*, R-V88-M18, R-V88-V35, R-V88-Y7777. African samples aren't older, as you said above, than 5000 years, and very likely also less.

So didn't R1b-V88 spread into Africa during the Sahara Subpluvial Age ? It ended at +-5000 years ago so I can not really see how it can be much younger than that in that. I think R1b-V88 introduced domesticated cattle to Northern Africa as early as the start of the Subpluvial +-9000 years ago.

@ Jomon, generally agree with what you're saying generally here about distro. of y, and decoupling though to put dates on the splits, check out Fig 3 and Fig 7 https://link.springer.com/article/10.1007/s00439-017-1773-z.

Split of R-Q from other K also 45,000 YBP, then almost simultaneous split of Q, R and Mal'ta R around 30,000 YBP. As you say "almost the same age of Mal'ta remains" just some would say 45,000 YBP vs 30,000 YBP is not what they would think of as ancient vs young.

Split of R1 into R1a and R1b around 25,000 YBP. (Same general time as I1 and I2+I3 split). Internal split of R1 and split of R from Mal'ta R also sets limits for split off of R2 to happen around 27,500 YBP.

Chadian R1b (V88) splits off around 18,000 YBP. (Do not seem to split from other R1b 5,000 YBP, unless we're talking about internal structure within V-88, where that may be a true split date for internal clade structure).

Changing mutations rates highly would make it difficult to incorporate all ancient sample dates (Ust Ishim and Dolni Vestonice would be particularly hard to fit to any slower rate).

C is ancient, since it arose ~ 60 Ky ... I read that the split from R to P1 occurred ~ 27 Ky ... however, based on the time of divergence within hap Q ... this date is wrong and ok I wrote a lot of shit ...I agree and will erase my coments...

In the Sahel and eastern Africa, a mixture of Western Eurasia comes from Levantine Neolithic (see Lazaridis et al., 2016) ... Neolithic was a very dynamic period with homogenization of populations. In this period the Levantines were no longer WGH-like + basal eurasian ... haussa has <7% of western eurasian inheritance and may reach 80% of R1b (aDNA and yDNA divergents).

The Villabruna sample (~ 14 Ky) already had subclade R1b and ANE blend ... no coincidence... To conclude, I don't believe that the ANE in its pure form was the source of all R1a/b by rapid migration ... I believe that this haps have arisen in Siberia and is slowly transmitted to HG pop by migrations and continuous mixing, generating steadly trend E-W with respect to ANE and R...this finding is supported by analysis of dimension 2 of PCA from Haak et al, 2015, which ANE-EHG-SHG-WHG forms a fairly clear trend, with La Braña and Samara HG as endmembers in the case of HG lineage ...

@ Jomon, no need to remove anything, interesting to read your thoughts. One other reason it seems like Chad R1b-V88 raises some questions are some of the finding in the recent paper on Chadic autosomes - http://www.cell.com/ajhg/fulltext/S0002-9297(16)30448-7

The Figure 4 has a finding where the Toubou population in Chad has strong offsets compared to the Amhara in being relatively more related to North Africans (strongly), Europeans,and European Hunter Gatherers (more weakly).

(This is relative as the Toubou have 20-30% West Eurasian ancestry, while Amhara around 40-50%. This looks about similar to Toubou's R1b, but they also have other haplogroups...).

This may suggest that migrations to Chad involved some degree of additional population from ancient Europe, via North Africa? (Or the same source that went to ancient Europe, if not ancient Europe). It will be good to see someone test models for them and see if they come out exactly the same as East Africans, or not.